MCMCtreeR (version 1.1)

estimateFixed: Fixed Age for MCMCtree analysis input

Description

Produce fixed age trees for MCMCtree analysis

Usage

estimateFixed(minAge, phy, monoGroups, writeMCMCtree = FALSE,
  MCMCtreeName = "estimateFixed.tre")

Arguments

minAge

vector of fixed age bounds for nodes matching order in monoGroups

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

• "parameters" estimated parameters for each node

• "apePhy" phylogeny in ape format with node labels showing node distributions

• "MCMCtree" phylogeny in MCMCtreeR format

• "nodeLabels" node labels in MCMCtreeR format

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Examples

# NOT RUN {
data(apeData)
attach(apeData)
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateFixed(minAge=minimumTimes[1],
monoGroups=monophyleticGroups[[1]], phy=apeTree)$MCMCtree
# }